Precursor scan mode

In precursor scan mode, the functions of Qj and are reversed. is set to a particular m/z, while Qj scans. This allows identification of all precursor ions that yield a particular product. A relevant example of such an application is the identification of phosphopeptides (Neubauer and Mann, 1999). Since phosphopeptides will lose PO3 fragments in the collision-induced dissociation step, Q3 is set at m/z 79 and Qj scanned. This allows identification of peptides that contain phosphate. Figure 3.10 includes the product and precursor ion spectra of such phosphopeptides. 

In a (B/E)(l - E) -scanning mode, a mass difference is seiected. For exampie, in this case a precursor ion m, is chosen (it is shown as being made up of two parts of mass mj, n,). After fragmentation, the product ion is mj accompanied by a neutral particle of mass n,. The mass difference (n, = m, - mj) can be specified so only pairs of ions connected by this difference are found. 

Advanced mass spectrometry enables the detection of higher-molecular-weight compounds that can be expected to retain more specific structure information contained in the original complex materials. The application of MS/MS using various scan modes will further extend the capabilities for identification of compounds in complex mixtures. Precursor scan techniques improve insight into the origin of ions in complex pyrolysates... 

Fig. 11.16. Representation of three tandem mass spectrometry (MS/MS) scan modes illustrated for a triple quadrupole instrument configuration. The top panel shows the attributes of the popular and prevalent product ion CID experiment. The first mass filter is held at a constant m/z value transmitting only ions of a single mlz value into the collision region. Conversion of a portion of translational energy into internal energy in the collision event results in excitation of the mass-selected ions, followed by unimolecular dissociation. The spectrum of product ions is recorded by scanning the second mass filter (commonly referred to as Q3 ). The center panel illustrates the precursor ion CID experiment. Ions of all mlz values are transmitted sequentially into the collision region as the first analyzer (Ql) is scanned. Only dissociation processes that generate product ions of a specific mlz ratio are transmitted by Q3 to the detector. The lower panel shows the constant neutral loss CID experiment. Both mass analyzers are scanned simultaneously, at the same rate, and at a constant mlz offset. The mlz offset is selected on the basis of known neutral elimination products (e.g., H20, NH3, CH3COOH, etc.) that may be particularly diagnostic of one or more compound classes that may be present in a sample mixture. The utility of the two compound class-specific scans (precursor ion and neutral loss) is illustrated in Fig. 11.17.

Fig. 11.17. Simulated mass chromatograms resulting from precursor ion and constant neutral loss tandem mass spectra (middle and bottom traces), illustrating the selectivity that those MS/MS scan modes can bring to chromatographic analyses. The top trace in the figure represents a total ion chromatogram obtained using a conventional single stage of mass analysis.

What are the three most common tandem mass spectrometry (MS/MS) scan modes (product ion scan, precursor ion scan, constant neutral loss scan). 

Skutlarek D, Faerber H, lippert F, Ulbrich A, Wawrzun A, Buening-Pfaue H (2004) Determination of glucosinolate profiles in Chinese vegetables by precursor ion scan and multiple reaction monitoring scan mode (LC-MS/MS). Eur Food Res Technol 219 643-649... 

A product ion scan can obtain stmctural information of a given precursor ion while a precursor ion scan is more suited to find stmctural homologues in a complex mixture. Bosentan (Mr = 551, Fig. 1.19) has two metabolites corresponding to the tert-butyl hydroxylation product (Mr = 567) and the dealkylation of the me-thoxy group to form the phenol (Mr = 537). Bosentan (Tracker, Actelion Phrama-ceuticals) is an oral duel endothelin receptor antagonist approved for the use in arterial hypertension [56]. Selection of the fragment at m/z 280 can fish out precursor ions corresponding only to bosentan and these two metabolites (Fig. 1.19C). A similar result is obtained with the constant-neutral loss scan mode (Fig. 1.19D) which is based on neutral loss of 44 units. 

In tandem MS mode, because the product ions are recorded with the same TOF mass analyzers as in full scan mode, the same high resolution and mass accuracy is obtained. Isolation of the precursor ion can be performed either at unit mass resolution or at 2-3 m/z units for multiply charged ions. Accurate mass measurements of the elemental composition of product ions greatly facilitate spectra interpretation and the main applications are peptide analysis and metabolite identification using electrospray iomzation [68]. In TOF mass analyzers accurate mass determination can be affected by various parameters such as (i) ion intensities, (ii) room temperature or (iii) detector dead time. Interestingly, the mass spectrum can be recalibrated post-acquisition using the mass of a known ion (lock mass). The lock mass can be a cluster ion in full scan mode or the residual precursor ion in the product ion mode. For LC-MS analysis a dual spray (LockSpray) source has been described, which allows the continuous introduction of a reference analyte into the mass spectrometer for improved accurate mass measurements [69]. The versatile precursor ion scan, another specific feature of the triple quadrupole, is maintained in the QqTOF instrument. However, in pre-... 

A Q-TOF spectrometer is similar to a triple quadrupole but Q3 is replaced by an orthogonal TOF mass spectrometer. Using a Q-TOF instrument only the product ion scan mode can be collected, but because of its high resolving power, accurate masses for both the precursor ion and product ions can be obtained. (See the section below on accurate mass measurements.)... 

Different MS MS experiments of product ion scan, precursor ion scan, and neutral loss scan modes of selected flavonoids can be carried out in order to confirm the structure of flavonoids previously detected by the full-scan mode. In the product ion scan experiments, MS MS product ions can be produced by CID of selected precursor ions in the collision cell of the triple-quadrupole mass spectrometer (Q2) and mass analyzed using the second analyzer of the instrument (Q3). However, in the precursor ion scan experiments, Q1 scans over all possible precursors of the selected ion in Q3 of the triple quadrupole. Finally, in neutral loss... 

Acylcarnitine analysis is performed as precursor scan in positive ion mode. Q1 is set to scan a mass range from m/z 200 to 500 m/z, while Q3 is set to determine a precur-... 

As an example of specificity improvement, Fig. 5.3.3 shows the full scan and product-ion MS/MS spectrum for 8-dehydroestriol, a prenatal hallmark of a fetus affected by Smith-Lemli-Opitz syndrome (SLOS), usually found in low concentrations. When using full scan mode, the detection of the most abundant ions (m/z 412, 397, 322, and visual appearance of the full spectrum) was compromised by the high background (Fig. 5.3.3, left). In contrast, acquisition in MS/MS mode (precursor ion m/z 412) provides a cleaner mass spectrum and a superior signal to noise ratio, especially for the transition product ion m/z 322 (Fig. 5.3.3, right). 

Several scan modes are unique to the triple-quadrupole instrument, and most of these modes are superior in duty cycle versus an ion trap, Fourier transform (FT), or time-of-flight (TOF) mass spectrometers. Different elements of the triple-quadrupole perform different operations for each scan mode. These scan modes, each of which will be described in detail, are single-reaction monitoring (SRM) or multiple-reaction monitoring (MRM), precursor ion scanning (PIS), and constant-neutral-loss scanning (NLS). These scan modes and applications for structural elucidation have been described in detail (Yost and Enke, 1978, 1979). 

It is important to first note that many classical clinical assays have traditionally measured one metabolite to detect one disease. Consequently, many of the rules of method validation were designed around this premise. MS/MS, as originally designed, detected two classes of compounds, amino acids and acylcamitines, in four to five different MS methods (known as scan modes such as neutral loss, precursor ion, or selected reaction monitoring), for approximately 500 distinct masses, more than 70 known compounds, and 20-30 stable isotope internal standards. How then did one approach such a complicated validation to gain acceptance as a reliable, useful method The answer is quite simple - start simply and compare to what was already established. 

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